Figure 4

Assessing parameter estimation using simulations. Left: boxes show the median and quartiles of the distribution of parameter estimates for 100 simulations. The 'true' value used in the simulation is shown in red. Right: boxes show the distribution of the bias (estimated value – real value), as a function of the (pooled) real values of the branch length. θ_*: GC content, ω GC content at root, α : shape of the Gamma distribution of rates across sites, p proportion of invariant sites (see text for details on the model used).